Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo

Genus Diadema (Family Diadematidae) is among the most widely dispersed and ecologically vital sea urchins and they are the bioindicators in coral reefs and seagrass bed ecosystems. Although Diadema urchins had been widely studied, knowledge about their evolutionary process, population structure and...

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Main Author:	Nursyuhaida, Md Shahid
Format:	Thesis
Language:	English
Published:	2021
Subjects:	QH301 Biology QH426 Genetics QL Zoology
Online Access:	http://ir.unimas.my/id/eprint/37873/4/Nursyuhaida%20Md%20Shahid.pdf
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id	my-unimas-ir.37873
record_format	uketd_dc
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	QH301 Biology QH426 Genetics QL Zoology
spellingShingle	QH301 Biology QH426 Genetics QL Zoology Nursyuhaida, Md Shahid Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
description	Genus Diadema (Family Diadematidae) is among the most widely dispersed and ecologically vital sea urchins and they are the bioindicators in coral reefs and seagrass bed ecosystems. Although Diadema urchins had been widely studied, knowledge about their evolutionary process, population structure and intraspecific variation are less known. Phylogenetic and population structure analysis have been conducted using COI gene sequences to infer variation within and between population, and statistical analysis have been conducted to validate morphological differences within D. setosum. At the very beginning of this study, Diadema is hypothetically monophyletic based on COI gene analysis. D. setosum formed a monophyletic clade comprised of all individuals and further divided into two subclades, separating Red Sea population (D. setosum-b) from those of Indo west Pacific (D. setosum-a). D. palmeri, D. clarki, and the other five species (D. mexicanum, D. antillarum, D. paucispinum, D. africanum and D. savignyi) further formed their own subclades supported by high bootstrap value thus supporting interspecific variation. Population structure of D. setosum from Malaysian Borneo revealed two distinct geographical clades which separates Sabah populations (Clade II) from Sarawak populations (Clade I) following the theory of isolation by distance as genetic divergence values have direct correlation with geographical distances. Significant pairwise differentiation of estimated ΦST value, Da (COI = 1.85%) and lack of shared haplotypes between the two populations further suggest that historical events have had strong effects on the population structure of D. setosum. Findings suggests that Tanjung Datu undergo population reduction due to historical or recent bottleneck events based on the small and significant of the SSD and Harpending’s raggedness, positive and lack of significance of the Tajima’s D and the Fu’s Fs value based on mitochondrial analysis. Findings suggests that historical events of the West Baram Line, the Lupar Line, oceanic currents of the South China Sea, the SCS Southern Anticyclonic Gyre and transoceanic ship transport have strong effects on the population structure of D. setosum in Malaysian Borneo. In Satang Island, Sarawak, the existence of D. setosum morphotypes with white primary spines, green secondary spines and white peristomial membrane has raised concern over the issue on cryptic species complex and whether the island’s ecological factors are the reason for the existence of D. setosum morphotypes. COI gene analysis suggest that white spines D. setosum samples found in Satang Island, Sarawak is a subspecies to D. setosum based on the formation of subclade and high genetic divergences between morphotypes, with significant differences in size, length-weight relationship, growth pattern as well as adaptability to environmental changes. Morphological data revealed the lack of significant differences between black spine and white spine D. setosum based on the twelve morphological characteristics however, subtle but identifiable distinctions of white primary spines, green secondary spines and white peristomial membranes were observed. The occurrences of D. setosum morphotypes in Satang Island, Sarawak might be due to the response of species to the environment in a specific scale as in Satang Island, Sarawak and the species may respond differently at larger scale which might be associated with habitat adaptation, natural selection or a physiological adaptation to ecological surrounding. Findings believes that cryptic species complex occurred in D. setosum with high morphological variability, due to fluctuating selection where high morphological polymorphism retained, causing the absence of some diagnostic characteristics of D. setosum such as the black spines and black peristomes. It is perceptible that COI gene is a suitable marker to infer genetic divergences at genus level, population structure and intraspecific variation. Keywords: Diadema, D. setosum, population structure, morphotypes, COI gene
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Nursyuhaida, Md Shahid
author_facet	Nursyuhaida, Md Shahid
author_sort	Nursyuhaida, Md Shahid
title	Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
title_short	Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
title_full	Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
title_fullStr	Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
title_full_unstemmed	Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo
title_sort	phylogenetic reconstruction of the sea urchin (genus diadema) and population genetic of diadema setosum in malaysian borneo
granting_institution	Universiti Malaysia Sarawak
granting_department	Faculty of Resource Science and Technology
publishDate	2021
url	http://ir.unimas.my/id/eprint/37873/4/Nursyuhaida%20Md%20Shahid.pdf
_version_	1783728492029935616
spelling	my-unimas-ir.378732023-04-10T04:02:04Z Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo 2021-02-08 Nursyuhaida, Md Shahid QH301 Biology QH426 Genetics QL Zoology Genus Diadema (Family Diadematidae) is among the most widely dispersed and ecologically vital sea urchins and they are the bioindicators in coral reefs and seagrass bed ecosystems. Although Diadema urchins had been widely studied, knowledge about their evolutionary process, population structure and intraspecific variation are less known. Phylogenetic and population structure analysis have been conducted using COI gene sequences to infer variation within and between population, and statistical analysis have been conducted to validate morphological differences within D. setosum. At the very beginning of this study, Diadema is hypothetically monophyletic based on COI gene analysis. D. setosum formed a monophyletic clade comprised of all individuals and further divided into two subclades, separating Red Sea population (D. setosum-b) from those of Indo west Pacific (D. setosum-a). D. palmeri, D. clarki, and the other five species (D. mexicanum, D. antillarum, D. paucispinum, D. africanum and D. savignyi) further formed their own subclades supported by high bootstrap value thus supporting interspecific variation. Population structure of D. setosum from Malaysian Borneo revealed two distinct geographical clades which separates Sabah populations (Clade II) from Sarawak populations (Clade I) following the theory of isolation by distance as genetic divergence values have direct correlation with geographical distances. Significant pairwise differentiation of estimated ΦST value, Da (COI = 1.85%) and lack of shared haplotypes between the two populations further suggest that historical events have had strong effects on the population structure of D. setosum. Findings suggests that Tanjung Datu undergo population reduction due to historical or recent bottleneck events based on the small and significant of the SSD and Harpending’s raggedness, positive and lack of significance of the Tajima’s D and the Fu’s Fs value based on mitochondrial analysis. Findings suggests that historical events of the West Baram Line, the Lupar Line, oceanic currents of the South China Sea, the SCS Southern Anticyclonic Gyre and transoceanic ship transport have strong effects on the population structure of D. setosum in Malaysian Borneo. In Satang Island, Sarawak, the existence of D. setosum morphotypes with white primary spines, green secondary spines and white peristomial membrane has raised concern over the issue on cryptic species complex and whether the island’s ecological factors are the reason for the existence of D. setosum morphotypes. COI gene analysis suggest that white spines D. setosum samples found in Satang Island, Sarawak is a subspecies to D. setosum based on the formation of subclade and high genetic divergences between morphotypes, with significant differences in size, length-weight relationship, growth pattern as well as adaptability to environmental changes. Morphological data revealed the lack of significant differences between black spine and white spine D. setosum based on the twelve morphological characteristics however, subtle but identifiable distinctions of white primary spines, green secondary spines and white peristomial membranes were observed. The occurrences of D. setosum morphotypes in Satang Island, Sarawak might be due to the response of species to the environment in a specific scale as in Satang Island, Sarawak and the species may respond differently at larger scale which might be associated with habitat adaptation, natural selection or a physiological adaptation to ecological surrounding. Findings believes that cryptic species complex occurred in D. setosum with high morphological variability, due to fluctuating selection where high morphological polymorphism retained, causing the absence of some diagnostic characteristics of D. setosum such as the black spines and black peristomes. It is perceptible that COI gene is a suitable marker to infer genetic divergences at genus level, population structure and intraspecific variation. Keywords: Diadema, D. setosum, population structure, morphotypes, COI gene Universiti Malaysia Sarawak (UNIMAS) 2021-02 Thesis http://ir.unimas.my/id/eprint/37873/ http://ir.unimas.my/id/eprint/37873/4/Nursyuhaida%20Md%20Shahid.pdf text en validuser phd doctoral Universiti Malaysia Sarawak Faculty of Resource Science and Technology Ministry of Higher Education of Malaysia (MyPhD)

Phylogenetic Reconstruction of the sea Urchin (Genus Diadema) and Population Genetic of Diadema setosum in Malaysian Borneo

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